Dear Dilip,

it's difficult to exactly analyse the coordination of your metal in 2D. But, my suggestion is :
Try another metal like Zn, which maybe is a contamination (from the plastic of eppendorf for example). Zn has more electron than Mg maybe that's the reason why it's still "green".
I suggest that you calculate anomalous difference map, maybe it could help, depending of the wavelenght used for data-collection.
And you can also try this phenix.refine which has an algorithm to build solvent.

Hope to help.

Nicolas
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De : CCP4 bulletin board [[log in to unmask]] de la part de Dilip Kumar [[log in to unmask]]
Envoyé : jeudi 9 juillet 2015 11:35
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Objet : [ccp4bb] Ambiguous metal ion at active site.

Dear All

I have solved a structure of a metal-ion dependent exonuclease enzyme. In homologous structures, two or three Manganese ions are present at catalytic center. However, I have used 2 mM MgCl2 in protein purification buffer. I tried to fit both of these metal ions at catalytic center but in both cases it still shows green density (Sigma level ~ 7) in difference map and low b-factor (<10) for these metal ions. For better understanding I have attached the screenshot of metal ions with difference map on. Please suggest me the possible reasons or methods to validate the presence of any other metal ions at catalytic center.

Thanks in advance.

Regards
Dilip Kumar
Research Associate
Chemical and Systems Biology Unit
CSIR-Institute of Genomics & Integrative Biology
Delhi-110025